GEO DataSets

(Submitter supplied) Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues, but their identification and organogenesis-related function have not elucidated. In this study, high-throughput sequencing was performed at three different organogenesis stages of zebrafish embryos, which were important for zebrafish muscle development. The three stages were 10 hpf (hours post fertilization) (T1), 24 hpf (T2) and 36 hpf (T3).

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30277

6 Samples

Download data: XLS

(Submitter supplied) Background/Aims:The ability of regeneration varies widely from invertebrates to vertebrates. Some animals, for example, flatworms, newts, salamanders, and lower vertebrates have the outstanding ability to regenerate all the organs even the whole individual. Unfortunately, the regenerative capacity of humans extremely attenuates along with the biological evolution and this makes it difficult for humans to recover from damaged or missing organs or tissues, and even cause serious loss of function or death. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21741

9 Samples

Download data: FA, TXT

(Submitter supplied) Y box-binding protein 1 (Ybx1) is critical for embryogenesis and organogenesis. In zebrafish, we identify Ybx1 is predominantly expressed in the enterocytes of intestine in day5 larvae, whereas its immediately degradation driven by ubiquitination on day6. Here we show the maternal lethality with cardiac edema in ybx1-/- larvae, and postnatal larval lethality exhibited in ybx1-/- larvae within the death window from 10dpf to 20dpf. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

9 Samples

Download data: CSV, TAB

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Danio rerio

Type:

Non-coding RNA profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL14875 GPL9319

20 Samples

Download data

(Submitter supplied) Long non-coding RNAs (lncRNAs) comprise a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins. Recent genome-wide studies in human and mouse have annotated lncRNAs expressed in cell lines and adult tissues, but a systematic analysis of lncRNAs expressed during vertebrate embryogenesis has been elusive. To identify lncRNAs with potential functions in vertebrate embryogenesis, we performed a time series of RNA-Seq experiments at eight stages during early zebrafish development. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL14875

3 Samples

Download data

(Submitter supplied) Long non-coding RNAs (lncRNAs) comprise a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins. Recent genome-wide studies in human and mouse have annotated lncRNAs expressed in cell lines and adult tissues, but a systematic analysis of lncRNAs expressed during vertebrate embryogenesis has been elusive. To identify lncRNAs with potential functions in vertebrate embryogenesis, we performed a time series of RNA-Seq experiments at eight stages during early zebrafish development. more...

Organism:

Danio rerio

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL14875 GPL9319

17 Samples

Download data

(Submitter supplied) We performed methylated RNA immunoprecipitation followed by sequencing (MeRIP–seq) combined with transcription sequencing to clarify the mechanism underlined YTHDF3 in CRC

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

8 Samples

Download data: XLSX

(Submitter supplied) Analysis of RNA-seq-based differential expression after overexpression of GAS5 or knockdown of YAP revealed a highly significant overlap of common targets.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

6 Samples

Download data: TXT

(Submitter supplied) The analysis of the RNA-binding protein immunoprecipitation sequencing (RIP-seq) experiment is performed to identified YAP-specific binding lncRNAs.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

2 Samples

Download data: XLS

(Submitter supplied) To investigate the expression profile of three different developental stages of zebrafish embryos, we then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different developmental of zebrafish embryos.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

6 Samples

Download data: TXT

(Submitter supplied) To experimentally-validate the non-coding status of annotated lncRNAs, we performed ribosome profiling over a developmental timecourse that matched our previously-published (Pauli et al. 2012) developmental transcriptome. We find that many previously-annotated lncRNAs appear to be translated, but in a pattern more akin to 5' leaders of coding genes.

Organism:

Danio rerio

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL14875

8 Samples

Download data: BW, GTF, TXT

(Submitter supplied) Genome-wide CRISPR screens identified lncRNAs that promote cell proliferation in HeLa, Huh7, and MCF7 cells

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

30 Samples

Download data: TXT

(Submitter supplied) Adrenocortical carcinoma (ACC) is an aggressive malignancy with high rates of recurrence following surgical resection. Long noncoding RNAs (lncRNAs) play an important role in cancer development. Pathogenesis of adrenal tumours has been characterised by mRNA, microRNA and methylation expression signatures but it is unknown if this extends to lncRNAs. We sought to describe lncRNA expression signatures in adrenocortical carcinoma (ACC), adrenal cortical adenoma (ACA) and normal adrenal cortex (NAC). more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL16956

21 Samples

Download data: TXT

(Submitter supplied) We have used RNA-seq to examine long non-coding RNA (lncRNA) and mRNA from rRNA depleted in chicken leg musle of three different development stages (11 embryo age, 16 embryo age, and 1 days post hatch). Our study reveals the prevalence of lncRNA in chicken, and has identified lncRNA differentially abundant in different stage of embryonic skeletal muscle, suggesting its important functions during poultry muscle development.

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19005

6 Samples

Download data: XLS, XLSX

(Submitter supplied) Long non-coding RNAs (lncRNAs) are a class of transcribed RNA molecules greater than 200 nucleotides long. Though do not encode proteins, they play functional roles in gene expression regulation. LncRNAs are notably abundant in the brain, however, their neural functions are largely unknown. Here we demonstrate that repeated short- and long-term cocaine administrations all decreased the expression of lncRNA Gas5 in the nucleus accumbens (NAc) of adult male mice. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: TXT

(Submitter supplied) We performed a genome-wide analysis of lncRNA expression in hepatoblastoma tissues to identify novel targets for further study of hepatoblastoma.We found that 2736 lncRNAs were differentially expressed in hepatoblastoma tissues.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17843

8 Samples

Download data: TXT

(Submitter supplied) EphrinA1 overexpression-induced gene signature was significantly enriched in the cells with high expression of GMAN

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13497

3 Samples

Download data: TXT

(Submitter supplied) To explor the role of lncRNAs in gastric cancer progression, we performed a microarray analysis to systematically screen the differential expression of lncRNAs between six human gastric cancer tissues and their matched non-tumor tissues

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL11269

12 Samples

Download data: PAIR

(Submitter supplied) EphrinA1 silencing-induced gene signature was significantly enriched in GMAN-depleted cells

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13497

3 Samples

Download data: TXT

(Submitter supplied) We report the application of single-molecule-based sequencing technology for high-throughput profiling of lncRNA in mouse cells. By obtaining over 47 million bases of sequence, we identified 3,307 lncRNAs based on single-cell RNA sequencing (RNA-Seq) data, discovered 52 lncRNAs that were significantly differentially expressed, and then selected 10 lncRNAs for qRT-PCR validation. Furthermore, we found that 12 lncRNAs with the target gene Tubb4b or Actn4 might be related to the expression of microtubule and microfilament proteins and the binding relationship was confirmed in a dual-luciferase reporter assay. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: FA, TXT